Hi,
I'm a new user of spm8 fieldmap toolbox ver. 2.1. I use Siemens Prisma 3T to collect fieldmap and want to use it for EPI distortion correction. It produced 2 magnitude images and 1 phase image (result from subtraction of two images). My questions are with double question marks and please if possible correct my concept.
My first question is, I think I should perform fieldmap correction and then do preprocessing (realignment, coregistration, normalization, ...etc). Is it correct??
Then, in spm8, I open batch --> tools --> FieldMap. Below is my input data by order:
In "Presubtracted phase and Magnitude data":
Phase image: phase image (the result from subtraction of two images)
Magnitude image: the magnitude image with the shorter echo time
Fieldmap defaults: Defaults values
Echo time: 10.00 12.46
Mask brain: should I select "no brain masking" or, if I select "Mask brain", what should I select to enter??
Blip direction: -1 (because the phase-encoding direction of my fieldmap is from right to left. Is it correct??)
Total EPI readout time: It is weird that the terminal of Prisma scanner (i.e. in "sequence" page) does not show the value of echo spacing. How come?? The fieldmap is 128x128, so I think the total EPI readout time should be 128*(echo spacing time).
EPI-based fieldmap: non-EPI based
Jacobian modulation: do not use
EPI sessions/select EPI to unwarp: I randomly select a single EPI image (called EPI_1) from my EPI data
Match VDM to EPI?: match VDM (no now field map data would be coregistered to EPI_1, right?)
Write unwarped EPI?: Write unwarped EPI
Select anatomical image for comparison: I select the T1 image of that subject. Am I correct??
Match anatomical image to EPI?: match anat
In “Apply VDM”:
Images: should I select all the EPI images I want to unwarp using field map data??
Fieldmap: the output vdm* file created from the fieldmap toolbox described above
Reslice Options/Reslice which images?: should I select "all images + mean images" or "all images"? what's the difference between both? I think because in the following preprocessing procedures (1) I will use mean images as the reference of coregistration for T1 and (2) all images should be corrected by field map for the following preprocessing, I should select "all images + mean images". Am I correct??
Masking: should I select Mask or don't mask? what's the difference??
Thank you so much.
Mike
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